Dear NWChem community,
I would like to perform QM/MM simulations in the NPT ensemble, so I want to use the isotherm and isobar keywords as such:
echo
start lpxrlps
memory 3750 mb
permanent_dir ./perm
scratch_dir ./data
charge -2
prepare
system lpxrlps
source qmmm_opt.pdb
new_top new_seq
new_rst
amber
update lists
ignore
crop
vacuo
cube
write lpxrlps_final.pdb
write lpxrlps_final.rst
end
task prepare
basis "ao basis"
* library "6-311++G(2d,2p)"
end
dft
xc becke88 lyp
disp vdw 2
end
md
system lpxrlps_final
noshake solute
cutoff 1.0
isotherm 0.0 50.0 anneal 0 10
isobar anisotropic
equil 0 data 100000
record rest 1000 prop 200
print step 1000 energies 1000 timing
mwm 3000
msa 3000
end
qmmm
#bq_zone 3.0
link_atoms hydrogen
region mm
density espfit
print low
end
task qmmm dft dynamics
However, the thermostat works as it should, the system reaches the temperature of 50K in 10 ps, but the barostat does not. The Volume of the cell changes as it should, but the pressure is always inexistent. Any clue why please ?
MOLECULAR DYNAMICS STATISTICAL INFORMATION 04/08/19 12:52:49
Statistics over last 100 steps Statistics over last 69400 steps
Average RMS fluct Drift/ps Average RMS fluct Drift/ps
Step 6.93505E+04 2.88661E+01 1.00000E+03 3.47005E+04 2.00341E+04 1.00000E+03
Time 6.93505E+01 2.88661E-02 1.00000E+00 3.47005E+01 2.00341E+01 1.00000E+00 ps
Number solvent-solvent interactions SR 9.44060E+05 1.21237E+02 3.64978E+03 9.43892E+05 5.49050E+03 4.05594E+01
Number solvent-solute interactions SR 2.92883E+04 2.36681E+01 7.42604E+02 2.89592E+04 7.99686E+02 1.83676E+01
Number solute-solute interactions SR 1.78701E+06 1.03978E+03 -1.17850E+04 1.78632E+06 1.15312E+04 1.00680E+02
Number of solvent SHAKE iterations 2.30000E+01 0.00000E+00 0.00000E+00 2.30000E+01 0.00000E+00 0.00000E+00
Number of solute SHAKE iterations 1.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 0.00000E+00 0.00000E+00
Volume 5.60430E+02 1.50232E-03 -5.20444E-02 5.62238E+02 1.04602E+00 -5.22122E-02 nm**3
Mass density 9.21245E+02 2.46962E-03 8.55514E-02 9.18287E+02 1.70844E+00 8.52766E-02 kg/m**3
Pressure 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Pa
Pressure scaling 1.00000E+00 3.57628E-08 -1.41895E-10 1.00000E+00 1.33620E-06 -2.19669E-14
Temperature 5.03586E+01 1.07094E-01 -1.77154E+00 4.67108E+01 1.02726E+01 2.81696E-01 K
Temperature solvent 5.23474E+01 1.19601E-01 -2.12244E+00 4.92026E+01 1.06985E+01 2.71719E-01 K
Temperature solute 3.78299E+01 2.37015E-01 4.38967E-01 3.10133E+01 8.42211E+00 3.44547E-01 K
Temperature scaling solvent 9.99964E-01 1.05542E-05 1.69261E-04 9.99928E-01 3.76834E-04 3.52933E-06
Temperature scaling solute 9.99964E-01 1.05542E-05 1.69261E-04 9.99928E-01 3.76834E-04 3.52933E-06
Energy electrostatic -1.02184E+06 1.64155E+02 -2.97199E+03 -1.01985E+06 4.02234E+03 -7.57518E+01 kJ/mol
Energy van der Waals 1.90906E+05 7.70287E+01 2.23573E+03 1.90449E+05 2.42266E+03 2.16429E+01 kJ/mol
Energy potential -8.15577E+05 1.20445E+02 -7.35257E+00 -8.14492E+05 1.70843E+03 -3.41574E+01 kJ/mol
Energy kinetic 2.23128E+04 4.74509E+01 -7.84934E+02 2.06966E+04 4.55158E+03 1.24814E+02 kJ/mol
Energy total -7.93264E+05 1.18219E+02 -7.92286E+02 -7.93796E+05 4.89705E+03 9.06563E+01 kJ/mol
Energy solvent intra electrostatic 8.00226E+04 5.29870E-03 1.14452E-05 8.00226E+04 1.07517E-01 -2.98113E-09 kJ/mol
Energy solvent intra van der Waals 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent inter electrostatic -1.02955E+06 1.68776E+02 -5.34967E+03 -1.02829E+06 3.62928E+03 -3.98854E+01 kJ/mol
Energy solvent inter van der Waals 1.98509E+05 1.79580E+02 5.94636E+03 1.98047E+05 2.46009E+03 2.39727E+01 kJ/mol
Energy solvent bonds 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent Urey-Bradley 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent proper dihedrals 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent improper dihedrals 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent polarization 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solvent kinetic 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Synchronization time 6.14134E-01 6.92574E-04 7.66764E-03 6.12599E-01 1.46251E-02 1.02834E-04 s
Efficiency load balancing 6.24514E-01 5.05986E-04 -4.60465E-03 6.25399E-01 7.73531E-03 -2.76474E-05
Time per step 1.02023E-01 9.98730E-05 4.25538E-04 1.01943E-01 2.11167E-03 9.53778E-06 s
Virial tensor element (1,1) 3.62884E+03 2.83709E+03 -6.38592E+04 7.41023E+03 1.10082E+04 -7.23803E+01 kJ/mol
Virial tensor element (1,2) 4.16092E+02 1.29996E+03 -1.19229E+04 4.75343E+01 2.73744E+03 -3.03380E+00 kJ/mol
Virial tensor element (1,3) 1.38631E+03 2.08358E+03 2.26396E+04 -5.49481E+01 2.75911E+03 6.06271E+00 kJ/mol
Virial tensor element (2,1) -1.62888E+02 1.48658E+03 6.83396E+03 4.93389E+01 2.03736E+03 -3.18339E+00 kJ/mol
Virial tensor element (2,2) 7.31643E+03 1.55091E+03 -2.17750E+04 7.37955E+03 1.05499E+04 -7.26116E+01 kJ/mol
Virial tensor element (2,3) 1.10492E+03 1.01569E+03 9.43030E+03 1.46326E+02 2.56136E+03 -1.14052E+01 kJ/mol
Virial tensor element (3,1) 2.63517E+03 7.90277E+02 1.99656E+04 -4.09244E+01 2.00545E+03 4.99824E+00 kJ/mol
Virial tensor element (3,2) 2.10967E+02 2.52140E+03 -6.21242E+04 1.44224E+02 2.58464E+03 -1.14857E+01 kJ/mol
Virial tensor element (3,3) 6.71529E+03 1.55520E+03 -7.08470E+03 7.33333E+03 1.02834E+04 -6.78269E+01 kJ/mol
Kinetic energy element (1,1) 3.20234E+03 1.56951E+01 -3.61642E+01 3.23207E+03 5.58239E+02 3.15388E+00 kJ/mol
Kinetic energy element (1,2) -1.21480E+01 1.46064E+01 -3.19518E+02 -1.30466E+00 2.87388E+01 4.35502E-02 kJ/mol
Kinetic energy element (1,3) 1.38983E+01 2.41651E+01 7.66891E+02 -3.18204E+00 2.63110E+01 4.15819E-02 kJ/mol
Kinetic energy element (2,1) -1.21480E+01 1.46064E+01 -3.19518E+02 -1.30466E+00 2.87388E+01 4.35502E-02 kJ/mol
Kinetic energy element (2,2) 3.20778E+03 1.82462E+01 6.07238E+02 3.23407E+03 5.58527E+02 3.26876E+00 kJ/mol
Kinetic energy element (2,3) -3.31860E+01 3.20500E+01 9.50668E+02 2.10884E+00 2.89197E+01 -1.11104E-01 kJ/mol
Kinetic energy element (3,1) 1.38983E+01 2.41651E+01 7.66891E+02 -3.18204E+00 2.63110E+01 4.15819E-02 kJ/mol
Kinetic energy element (3,2) -3.31860E+01 3.20500E+01 9.50668E+02 2.10884E+00 2.89197E+01 -1.11104E-01 kJ/mol
Kinetic energy element (3,3) 3.18349E+03 2.52527E+01 -8.38376E+02 3.22854E+03 5.66859E+02 3.42538E+00 kJ/mol
Energy solute 1 intra-electrostatic -1.02178E+05 1.28851E+02 1.24428E+03 -1.02156E+05 3.20820E+02 5.02955E+00 kJ/mol
Energy solute 1 intra-van der Waals -1.02809E+04 7.77849E+01 -2.53235E+03 -1.02848E+04 6.10100E+01 -1.43220E+00 kJ/mol
Energy solute 1-solvent electrostatic-2.36288E+04 9.15700E+01 2.49670E+03 -2.29802E+04 1.16159E+03 -4.08597E+01 kJ/mol
Energy solute 1-solvent van der Waals-1.73815E+03 4.26943E+01 -1.23335E+03 -1.71078E+03 1.00976E+02 -1.83592E+00 kJ/mol
Energy solute 1 bonds 1.42944E+03 2.41442E+01 5.83573E+01 1.22448E+03 1.81035E+02 8.39359E+00 kJ/mol
Energy solute 1 angles 3.82632E+03 3.18476E+01 3.09650E+02 3.62520E+03 2.29398E+02 9.61384E+00 kJ/mol
Energy solute 1 Urey-Bradley 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solute 1 proper dihedrals 1.00986E+04 2.30800E+01 3.60895E+02 1.00568E+04 7.39973E+01 1.94396E+00 kJ/mol
Energy solute 1 improper dihedrals 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 kJ/mol
Energy solute 1 van der Waals 3rd 4.41602E+03 1.38260E+01 5.50733E+01 4.39773E+03 4.02074E+01 9.38324E-01 kJ/mol
Energy solute 1 electrostatic 3rd 5.34941E+04 6.75502E+01 -1.36329E+03 5.35602E+04 8.51558E+01 -3.61960E-02 kJ/mol
Energy solute 1 van der Waals nb -1.02809E+04 7.77849E+01 -2.53235E+03 -1.02848E+04 6.10100E+01 -1.43220E+00 kJ/mol
Energy solute 1 electrostatic nb -1.02178E+05 1.28851E+02 1.24428E+03 -1.02156E+05 3.20820E+02 5.02955E+00 kJ/mol
Energy solute 1 kinetic 2.29625E+03 1.43867E+01 2.66450E+01 1.88249E+03 5.11216E+02 2.09138E+01 kJ/mol
Energy solute 1 potential -5.18779E+04 1.19911E+02 -1.23571E+03 -5.19218E+04 3.93445E+02 3.10305E+00 kJ/mol
|